En
  • دکتری (1385)

    بیو فیزیک

    دانشگاه تربیت مدرس،

  • کارشناسی‌ارشد (1380)

    زیست شناسی - بیوفیزیک

    دانشگاه تربیت مدرس،

  • کارشناسی (1376)

    زیست شناسی - علوم جانوری

    دانشگاه تهران، ایران

  • طراحی پپتیدهای دارویی و بیو فیزیک محاسباتی
  • شبیه سازی بافتهای مصنوعی

    داده ای یافت نشد

    ارتباط

    رزومه

    An experimental investigation on the influence of various buffer concentrations, osmolytes and gold nanoparticles on lysozyme: Spectroscopic and calorimetric study

    Soraya Mohammadi, Khosro Khajeh, Majid Taghdir, Bijan Ranjbar
    Journal PapersInternational Journal of Biological Macromolecules , Volume 172 , 2021 March 1, {Pages 162-169 }

    Abstract

    Considering importance and several industrial applications of lysozyme, including natural antibiotic and preservative, identifier for the diagnosis of diseases, and extraction purposes, its reversibility and stability studies can be very important. In this paper, the role that buffer and osmolytes concentrations play on the thermodynamic stability of lysozyme denaturation process, that is a new simple and inexpensive method, was evaluated by Nano-DSC III, far- and near-UV CD and fluorescence techniques. In thermal denaturation study, RI and ΔG of protein increased from 25.62% to 58.82% and 48.87 to 63.63?kJ?mol−1 with the increment of buffer and osmolytes concentrations, respectively. These changes showed a significant increase of 129.59

    Evaluation of transport mechanism of ascorbic acid through cyclic peptide-based nanotubes: a molecular dynamics study

    FA Joozdani, M Taghdir
    Journal Papers , , {Pages }

    Abstract

    Thermostability of Ctenophore and Coelenterate Ca2+-Regulated Apo-photoproteins: A Comparative Study

    R Nemati, M Molakarimi, A Mohseni, M Taghdir, K Khalifeh, R H. Sajedi
    Journal Papers , , {Pages }

    Abstract

    The trypsin inhibitor pro-peptide induces toxic effects in Indianmeal moth, Plodia interpunctella

    Seyed Ali Hemmati, Zeinab Takalloo, Majid Taghdir, Mohammad Mehrabadi, Saeed Balalaei, Saeid Moharramipour, Reza H Sajedi
    Journal PapersPesticide Biochemistry and Physiology , 2020 October 15, {Pages 104730 }

    Abstract

    The inhibitory potential of an inhibitor peptide based on the pro-region of trypsin zymogen was investigated in Indianmeal moth, P. interpunctella, which is a world-wide insect pest of stored food. Five peptides were designed based on molecular docking simulations. The designed peptide with the best score was selected and synthesized for further screening in vitro and in vivo. The peptide was characterized and its inhibitory effects towards the insect trypsin were evaluated and the kinetic analysis revealed a competitive type of inhibition against the target enzyme. The results showed that the peptide could successfully suppress the pest midgut trypsin, and more interestingly, it did not show considerable inhibitory effects on a mammalian t

    The physicochemical properties role of a functionalized alkyl-peptide in nanofibre formation and neural progenitor cells viability and survival

    Havva Mehralitabar, Majid Taghdir, Rezvan Mobasseri, Hossein Naderi-Manesh
    Journal PapersPolymer Testing , Volume 91 , 2020 November 1, {Pages 106829 }

    Abstract

    Amphiphilic alkyl-peptides as novel biomaterials form 3D scaffolds that are applicable in tissue engineering. Here, the nanofibre formation capability of a distinct alkyl-peptide was investigated using coarse-grained molecular dynamics simulation (CGMD) and experimental methods. The alkyl-peptide (Ace-FAQRVPPEEEGGGAAAAK-Nhe(C16)) was functionalized with a peptide epitope (FAQRVPPP) which can help to maintenance and differentiation of neural stem cells. Two alkyl-peptide systems were investigated: the all-functionalized system (with only bioactive alkyl-peptides) and the distributed system (a combination of bioactive and non-bioactive alkyl-peptides with ratio 1:2). The CGMD and TEM results confirm elongated nanofibres for all-functionalized

    Investigation of Atrial Natriuretic Peptide as A Competitive Inhibitory Candidate Against Wnt/β-Catenin Signalling: A Molecular Dynamics Approach

    Najme Dehghanbanadaki, Majid Taghdir, Hossein Naderi-Manesh
    Journal PapersInternational Journal of Peptide Research and Therapeutics , 2020 June 25, {Pages 11-Jan }

    Abstract

    Wnt/β-catenin signaling, a highly evolutionary conserved pathway, is abnormally regulated in many human cancers. This pathway is one of the proposed mechanisms of atrial natriuretic peptide (ANP) anti-cancer effect. ANP which at first reported as a cardio hormone, inhibits proliferation of different cancer cell lines and tumor growth in vitro and in vivo respectively. Previous studies have shown a possibility of direct interaction between ANP and Frizzled (FZD), the main extracellular receptor of the pathway, and so a competition between ANP and Wnt for binding to this receptor. Here, using a molecular dynamics approach, we investigated this hypothesis validity and also the probable mechanism involved. We found three overlapping binding r

    A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube

    Farzane Abasi Joozdani, Majid Taghdir
    Journal PapersJournal of Biomolecular Structure and Dynamics , 2020 April 13, {Pages 12-Jan }

    Abstract

    Cyclic peptide nanotubes (CPNTs) are open-ended, hollow, and tubular structures that are made of several cyclic peptide rings. These structures can act as a transmembrane channel and transport ions or small molecules. In this work, we studied the stability of a cyclic peptide nanotube 8 ? [(Trp-D-Leu)4-Gln-D-Leu] into a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol and also the transport mechanism of β-D-glucose through this nanotube was investigated. Our findings revealed that the CPNT was stable in the lipid bilayer during the simulation time and non-bonded interactions, especially hydrogen bonding have an important role to form a stable CPNT in the membrane. The glucose jumps from a Cα-region into the mid-Cα regio

    Structural Insight into the role of Inhibitor Peptide derived from Tumstatin-Integrin Complex in Inhibitory Mechanism: A Molecular Dynamics Simulations Study

    Majid Taghdir
    Journal PapersModares Journal of Biotechnology , Volume 11 , Issue 2, 2020 June 10, {Pages 137-144 }

    Abstract

    [1] On the activation of integrin αIIbβ3: Outside-in and inside-out pathways [2] Integrin signaling in control of tumor growth and progression [3] Integrin cytoplasmic tail interactions [4] Structural basis for distinctive recognition of fibrinogen γC peptide by the platelet integrin αIIbβ3 [5] Talin binding to integrin ? tails: A final common step in integrin activation [6] The final steps of integrin activation: The end game [7] Molecular dynamics simulations of forced unbending of integrin αVβ3 [8] Identification of amino acids essential for the antiangiogenic activity of tumstatin and its use in combination antitumor activity [9] High affinity vs. native fibronectin in the modulation of αvβ3 integrin conformational dynamics: In

    Study of the Effect of Multi-Walled Carbon Nanotube on Human Hepcidin 20 by Using Molecular Dynamics Simulation

    Reza Rasoolzadeh, F Mehrnejad, Majid Taghdir, P Yaghmaei
    Journal PapersModares Journal of Biotechnology , Volume 11 , Issue 1, 2020 March 10, {Pages 103-108 }

    Abstract

    The interactions between carbon nanotubes (CNTs) and proteins were considered much attention. Advanced CNT applied biomolecules require a mutual understanding of their interactions with biological molecules. Noncovalent interactions of blood peptides, such as hepcidin, with carbon nanotubes, have important effects in a wide range of biological applications that are detected by analyzing the thermodynamic parameters of the interaction between CNTs and peptides. In addition, the effects of different parameters in order to evaluate how the interaction of CNTs with peptide affects, structural changes and stability of peptides were studied. In this study, based on molecular dynamics (MD) simulation, the structural changes of hepcidin 20 in inter

    Tuning the active site dynamic properties and substrate affinity in Pseudomonas aeruginosa elastase by Cys270–Cys297 disulfide bond

    Zohreh Jahangirizadeh, Majid Taghdir
    Journal PapersChemical Physics , Volume 531 , 2020 March 1, {Pages 110615 }

    Abstract

    We decided to investigate the effect of the Cys270-Cys297 disulfide bond on catalytic site integrity of Pseudomonas aeruginosa elastase in its native state. We compared dynamical behaviour of the active site of this enzyme in the native and disulfide bond broken states by performing short timescale molecular dynamics simulations. Our results reveal that the disulfide bond involves in regulating of amplitude of fluctuations of functionally important residues and in tuning of their Φ and ψ dihedral angles values. Furthermore, the presence of this disulfide bond participates in the adjustment of the correlation of motions and the distance between pairs of active site residues. Docking simulation studies reveal that the breakage of the disulf

    Investigating the effect of solvent type on the formation of daunoxome liposome (DSPC-CHOL) using coarse-grained molecular dynamics simulation

    Jalil Parchekani Choozaki, Majid Taghdir
    Journal PapersJournal of Cellular and Molecular Research (Iranian Journal of Biology) , Volume 33 , Issue 3, 2020 September 22, {Pages 432-443 }

    Abstract

    Liposomes are widely used as carriers for a large number of molecules in pharmaceutical studies. The stability and formation of liposomes is important in the drug delivery, and can be influenced by the phospholipid composition of the liposomal membrane. In this study, we are trying to investigate the effect of solvent type on the formation of daunoxome liposome (DSPC-CHOL). For this purpose, a molecular dynamics simulation method was used. The analysis of the radial distribution function that was performed to determine the formation and distribution of lipids, properly demonstrated that daunoxome liposome created dense nano-disk structure in a polar water environment and a spherical liposome in a non-polar water environment, and that the ph

    Structural Insight into the Role of Inhibitory Peptide Derived from Tumstatin-Integrin Complex in Inhibitory Mechanism: A Molecular Dynamics Simulations Study

    M Ghorbani, M Taghdir
    Journal Papers , Volume 11 , Issue 100838, 2020 January 1, {Pages 137-144 }

    Abstract

    Integrin inhibitors may change the conformational and dynamical properties of integrin, but its molecular properties in this process are not clearly understood. Tumstatin is an anti-angiogenesis protein derived from collagen XVIII, but little is known about how Tumstatin applies its antiangiogenic and antitumor effects. It has been reported that 18 amino acids fragment of Tumstatin has antiangiogenesis and anti-tumor activities similar to Tumstatin. In this study, molecular docking and molecular dynamics simulations were used to describe the inhibitory activity of peptide at the molecular level. Peptide can bind to the Hybrid/EGF-4 interface which these interactions might contribute to improved hydrophobic interactions at these regions and

    Spectroscopic Studies on the Interaction of Gold Nanoparticles with Lysozyme

    Soraya Mohammadi, Khosro Khajeh, Majid Taghdir, Nasrin Farahani, Bijan Ranjbar
    Journal PapersBiomacromolecular Journal , Volume 5 , Issue 2, 2019 December 1, {Pages 140-151 }

    Abstract

    Gold nanoparticles are promising materials for biomedical applications because of the attractive optical properties such as the absorption and scattering of light at resonant wavelength. Due to the fruitful applications of gold nanoparticles (GNPs), they are appropriate for a variety of biological studies. One of the most important applications of nanoparticles is protein carriers, in which transport of therapeutically relevant protein is done to in vivo or in vitro targets. Protein folding and properties of probable intermediates during the folding of proteins had been investigated in several studies. The molten globule state, a main intermediate of protein folding, has native-like secondary but perturbation of tertiary structure. Conseque

    A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

    Havva Mehralitabar, Majid Taghdir, Hossein Naderi-Manesh
    Journal PapersJournal of Biomolecular Structure and Dynamics , Volume 37 , Issue 13, 2019 September 2, {Pages 3434-3444 }

    Abstract

    Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive a

    Investigation the Effect of Cholesterol on the Formation and Stability of the Liposomes using Coarse-Grained Molecular Dynamics Simulations

    J Parchekani Choozaki, M Taghdir
    Journal PapersModares Journal of Biotechnology , Volume 10 , Issue 2, 2019 July 10, {Pages 241-246 }

    Abstract

    Liposomes or biological vesicles are formed from cholesterol, phospholipids, and water. Also, sometimes other biological and non-biological molecules imported in the structure of liposome. The stability of the liposomes in the treatment of diseases and drug delivery, it is vitally important and can be influenced by the composition of phospholipid. In addition, the presence or absence of cholesterol may also affect the stability of liposome. Also, the formation of liposomes is affected by the presence or absence of cholesterol. In this study, we are seeking to affect the presence or absence of cholesterol on the stability and the formation of the liposome. For this purpose, the molecular dynamics simulation method is used. Liposomes that the

    Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations

    Maryam Molakarimi, Michael A Gorman, Ammar Mohseni, Zaiddodine Pashandi, Majid Taghdir, Hossein Naderi-Manesh, Reza H Sajedi, Michael W Parker
    Journal PapersJournal of Biological Chemistry , Volume 294 , Issue 1, 2019 January 4, {Pages 20-27 }

    Abstract

    Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca2+-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd2+-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 ? resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156–Arg-39–Tyr-202 triad creates a hydrogen-bonded network to facilitate

    Effects of single-walled carbon nanotube on the conformation of human hepcidin: molecular dynamics simulation and binding free energy calculations

    Reza Rasoolzadeh, Faramarz Mehrnejad, Majid Taghdir, Parichehreh Yaghmaei
    Journal PapersJournal of Biomolecular Structure and Dynamics , Volume 37 , Issue 8, 2019 May 24, {Pages 2125-2132 }

    Abstract

    The major regulator of systemic iron homeostasis is controlled by human Hepcidin, which is a 25 amino acid cysteine-rich cationic antimicrobial peptide (HAMP) hormone, that was first identified in both human blood ultra-filtrate and urine and has antibacterial and antifungal activities. Hepcidin is named because of it is synthesized in hepatocytes (hep-) and has antimicrobial properties in vitro (-cidin). Human Hepcidin is made by hepatocytes, while in recent studies; the synthesis of hepcidin has been detected in bacteria-activated neutrophils and macrophages, although at a lower level than in the hepatocytes (Aschi, Bozzi, Di Bartolomeo, & Petruzzelli, 2010). In human urine, the predominant form is derived from an 84 amino acid Hepcidin p

    A nanodisc structure design from sphingomyelin of chicken egg phospholipid (DPSM) and cholesterol (CHOL) and its formation study: a coarse-grained molecular dynamics simulation

    Jalil Parchekani Choozaki, Majid Taghdir
    Journal PapersJournal of Cellular and Molecular Research (Iranian Journal of Biology) , 2019 September 1, {Pages }

    Abstract

    Double-layer nanodiscs are structures made up of phospholipids double-layer membrane and do not exist between the double-layer of any contents or water molecules. Quadruple nanodiscs are actually like a normal cell that pushes on both sides of the body, such as the red blood cell structure that is pushing on both sides. The structure of nanodisc can cover water-soluble drugs in its hydrophilic superficial and fat-soluble drugs within its two layers, which is a hydrophobic environment. Synthesis of nanodiscs in experimental environments is time-consuming and costly. Therefore, in this research, the nanodisc structures from Egg sphingomyelin (DPSM) and Cholesterol (CHOL) molecules were designed and constructed. In order to do this goal, a mol

    Molecular cloning, prokaryotic expression, purification, structural studies and functional implications of Heat Shock Protein 70 (Hsp70) from Rutilus frisii kutum

    Zohreh Jahangirizadeh, Hossein Ghafouri, Reza H Sajedi, Sajjad Sarikhan, Majid Taghdir, Reyhaneh Sariri
    Journal PapersInternational journal of biological macromolecules , Volume 108 , 2018 March 1, {Pages 798-807 }

    Abstract

    A novel Hsp70 chaperone from Rutilus frisii kutum was identified, cloned, expressed, purified and its functional characteristics revealed. The 3D structure of Hsp70 from Rutilus kutum was constructed using the crystal structure of E. coli Hsp70 as the template, with 47% sequence identity. The in vitro ATPase activity assay after 60?min, ATP hydrolysis of purified recombinant Hsp70 (8?μM) was improved by binding to denatured thermally luciferase (3?μM) about 2.5-fold compared with that of Hsp70 alone. Based on the results, it was found that the purified Hsp70 chaperone was able to considerably suppress heat-induced aggregation of luciferase by binding to DnaJ co-chaperone (5?μM) more than 70% after 10?min at 42??C. In addition, Hsp70 DnaJ

    Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study

    Esmaeil Behmard, Parviz Abdolmaleki, Majid Taghdir
    Journal PapersBiophysical chemistry , Volume 233 , 2018 February 1, {Pages 47-54 }

    Abstract

    P7 is the only viral channel encoded by the Hepatitis C Virus (HCV) genome. It is a small, highly hydrophobic protein containing 63 amino acids. Structural studies have shown that p7 has two transmembrane (TM) α helices linked by a short dibasic cytoplasmic loop. P7, mostly placed in the endoplasmic reticulum (ER), is a membrane-associated protein. The results obtained from different studies revealed that p7 is a polytopic membrane protein that could oligomerize in membrane bilayer to create ion channels with cation selectivity. In addition, p7 is highly conserved and plays an important role in the assembly and release of mature viral particles. Thus, it can be considered as a potential target for anti-HCV drugs. It has been found that sev

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    دروس نیمسال جاری

    • دكتري
      مباحثي در بيوفيزيك ( واحد)
      دانشکده علوم زیستی، گروه بيو فيزيك
    • كارشناسي ارشد
      بيوفيزيك سلولي ( واحد)

    دروس نیمسال قبل

    • دكتري
      اندركنش ليگاند با پروتئين ( واحد)
      دانشکده علوم زیستی، گروه بيو فيزيك
    • 1398
      عظيمي, الگا
      بررسي ديناميك , ساختار و عملكرد گيرنده تيروزين كيناز EGFR در برهمكنش با مهاركننده انتخابي
    • مدیریت گروه زیست شناسی دانشگاه گیلان به مدت 2 سال
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